'\" t
.TH samtools-phase 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools phase \- call and phase heterozygous SNPs
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
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.
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.SH SYNOPSIS
.PP
samtools phase
.RB [ -AF ]
.RB [ -k
.IR len ]
.RB [ -b
.IR prefix ]
.RB [ -q
.IR minLOD ]
.RB [ -Q
.IR minBaseQ "] " in.bam

.SH DESCRIPTION
.PP
Call and phase heterozygous SNPs.

.SH OPTIONS
.TP 8
.B -A
Drop reads with ambiguous phase.
.TP 8
.BI -b \ STR
Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file
.BR STR .0.bam
and phase-1 reads in
.BR STR .1.bam.
Phase unknown reads will be randomly allocated to one of the two files. Chimeric reads
with switch errors will be saved in
.BR STR .chimeric.bam.
[null]
.TP
.B -F
Do not attempt to fix chimeric reads.
.TP
.BI -k \ INT
Maximum length for local phasing. [13]
.TP
.BI -q \ INT
Minimum Phred-scaled LOD to call a heterozygote. [40]
.TP
.BI "-Q,\ --min-BQ " INT
Minimum base quality to be used in het calling. [13]
.TP
.BI --no-PG
Do not add a @PG line to the header of the output file.

.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
